Layering

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To combine a couple sentences on page 60, I would define layering as:
usually achieved by a hierarchy of visual effects, enhances representation of both data dimensionality and density on flatland

In Tufte's examples, layering is usually portrayed through the use of color to distinguish different aspects of the graphic such as with the industrial diagram..

Separation seems to involve the use of white space or lines. Separation can be used incorrectly or correctly. Such as, the use of white space to create vibration effects or the use of lines to create an overbearing grid.

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Comments

Separation

I agree with your definition of separation, especially that it can be used incorrectly, as well as correctly. I've seen a lot of examples where the separation makes the design of the image ineffective.

Agreed

I would also that layering involves changing the "weight" of the graphic. It gives more prominence to certain elements over others.

Vibration Effects

You mentioned vibration effects. My understanding was that vibration means as you aim to locate a specific piece of information, vibration effects make the data seem to move up and down which effectively makes it difficult to keep your place visually because there are no clear visual anchor points near your piece of wanted information. Would you agree?

I'm glad you brought up

I'm glad you brought up flatland! I was so focused on the terms layering and separation that I completely forgot to mention flatland. I wonder is Tufte would consider a true flatland? Are there any true flatlands or simply improperly layered messes on top of flatland?